GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Pontimonas salivibrio CL-TW6

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_104913141.1 C3B54_RS02765 aldehyde dehydrogenase

Query= metacyc::MONOMER-15108
         (486 letters)



>NCBI__GCF_002950575.1:WP_104913141.1
          Length = 507

 Score =  348 bits (893), Expect = e-100
 Identities = 194/481 (40%), Positives = 279/481 (58%), Gaps = 14/481 (2%)

Query: 13  HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72
           H+I G++   + G  F++I+P   +    +A G A +ID A+ AA  A    W K +  E
Sbjct: 22  HWIGGQWTKPVKGNYFEDISPVNGKPFCEIARGTAEDIDAALDAAHAAAPA-WGKASTTE 80

Query: 73  RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132
           R AVL K+ D+I    E L+V E+ D GKP   + + DIP AA +F +F   +R    + 
Sbjct: 81  RAAVLNKIADVIDANVEMLAVAETWDNGKPIRETLNADIPLAADHFRYFVAAVRAQDGDF 140

Query: 133 TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192
            +MD     Y    P+GV+G I PWN P+L+  WKLAPAL+AGN VV+KPAE TP +  V
Sbjct: 141 QEMDGDTTAYHYHEPLGVVGQIIPWNFPILMAAWKLAPALSAGNAVVLKPAEQTPASILV 200

Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLK 252
           LAE+  D  +P GV+N+V+GFG   AG  L   P +  I+FTGETTTG++I+  A+  + 
Sbjct: 201 LAELIGDI-LPPGVLNIVNGFGA-EAGKPLASSPRIRKIAFTGETTTGRLILQYASANII 258

Query: 253 RLSYELGGKNPNVIFADSN------LDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEA 306
             + ELGGK+PN+ F D +       D+  E  +  +F NQGEVC C SR  +++  Y++
Sbjct: 259 PTTLELGGKSPNIFFDDVSQEKDDFYDKAQEGFVLFAF-NQGEVCTCPSRALIQKSHYDS 317

Query: 307 FLEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPE-- 364
           FL   V +TK+ + G+P D  T+VGA  S++  E++  YI +  +EG T++ GG R +  
Sbjct: 318 FLGDAVERTKKAIQGNPLDTDTQVGAQASNDQLEKILSYIDIGKQEGATLVCGGDRVDLG 377

Query: 365 -GLEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVW 423
             L  GY++EP I  G     R+ +EEIFGPVV V  FD  ++ ++  NDT YGL A VW
Sbjct: 378 GDLADGYYVEPAIFEG-NNKMRLFQEEIFGPVVAVTSFDDYDDAIQIANDTLYGLGAGVW 436

Query: 424 TNDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNIC 483
           + +   A+R    I+AG VWVN +        FGG K SGIGRE    +   Y +  N+ 
Sbjct: 437 SRNGNTAYRAGRDIQAGRVWVNNYHAYPAGAAFGGYKSSGIGRENNKLALSHYQQTKNLL 496

Query: 484 I 484
           +
Sbjct: 497 V 497


Lambda     K      H
   0.318    0.136    0.404 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 651
Number of extensions: 34
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 486
Length of database: 507
Length adjustment: 34
Effective length of query: 452
Effective length of database: 473
Effective search space:   213796
Effective search space used:   213796
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory